And influential forward Tom Hooper, who was seismic off the bench against Ireland, will also miss Saturday's Test against France in Brisbane due to a shoulder injury.
The 25-year-old Gordon, after being substituted with cramp in Saturday's 33-31 loss to Ireland, was set to have his fitness tested in Tuesday's session at Ballymore.
But the Queensland Reds' No.10, who battled leg issues during the Super Rugby Pacific season, was unable to take the field and subsequently scratched from Saturday's clash and next week's Test in Perth against Italy.
Gordon combined brilliantly with halfback Ryan Lonergan in a new partnership in Sydney, with the Wallabies' expansive offence opening up a 12-point lead that was ultimately mowed down.
Hooper, who starred for Exeter in England this year, was physical in his arrival after halftime in a like-for-like substitution with the rampaging Rob Valetini.
Replacement flyhalf Ben Donaldson took control in the final quarter of the Test once Gordon limped off and missed two long-range penalty attempts that would have clinched the game.
Brumbies playmaker Declan Meredith is also in camp and poised for a debut in Brisbane on Saturday night.
It continues the musical chairs theme at the Wallabies, who were unable to settle on a consistent playmaker during last year's rollercoaster 5-10 campaign.
Gordon was seriously injured during a stint in the NRL with Gold Coast, hospitalised with a spinal fluid leak, and has endured nagging leg injuries since returning to rugby a year ago.
"He played really well," teammate Fraser McReight said of Gordon.
"Devastated for him, but I guess injuries are a part of rugby and we've always said, 'next man up'.
"We've got Donno and Dec, both had great seasons pushing their case."Â
McReight argued that Donaldson's 20 Tests and Meredith's experience at the ACT Brumbies with halfback Lonergan meant there would be continuity regardless.
The flanker pointed to the 12 penalties conceded against Ireland - 11 in their own half - as key to Australia's downfall and has urged his side to be more clinical in Brisbane, particularly if they build a lead.
"When we had them by the throat we didn't go for the kill in the last five, 10 minutes of the first half," he said.
"When we've got them, keep them down. Be cool, calm ... Joe (Schmidt) talks about being blue-headed, not red-headed."
Incoming Wallabies coach Les Kiss was an interested observer on Tuesday as he prepares to take over following next week's Test against Italy in Perth.
Kiss had a say in the Wallabies' squad picked by Schmidt for this three-Test Nations Championship swing.
But he stayed well clear of the squad in Sydney and will only observe from the shadows in Brisbane and Perth before taking the reins ahead of an Osaka Test against Japan on August 8.
"It's a different feeling around the group, but that (handover's) in four weeks' time and we've got a job to do this weekend and next," McReight said.
Meanwhile, Six Nations champions France are expected to make some changes to the side the All Blacks pipped by two points in Christchurch on Saturday.
Winger Damian Penaud (calf) has returned home injured, but nine players who contested the Top 14 final have bolstered the touring party.
Among them are hulking New Zealand-born, Australian-raised lock Emmanuel Meafou - who played club rugby at Brothers with several current Wallabies - and Toulouse playmaker Romain Ntamack.
Meafou could take the place of Canberra product and former NSW Waratahs and Brumbies lock Tom Staniforth, who could come off the bench after starting in his French debut against New Zealand.
Flyhalf against the All Blacks, Matthieu Jalibert has a calf issue and is in doubt to face Australia.
Either the Bordeaux playmaker or La Rochelle's Antoine Hastoy could shift to fullback and make space for Ntamack in the No.10, with Aaron Grandidier-Nkanang a favourite to earn a spot on the wing.
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